SERTM1

Chr 13

serine rich and transmembrane domain containing 1

Also known as: C13orf36

NCBI Gene: 400120ENSG00000180440UniProt: A2A2V5

SERTM1 encodes a protein localized to intracellular membrane-bounded organelles, though its specific molecular function remains unclear. Mutations in this gene have been associated with neurodevelopmental disorders, but the clinical phenotype and inheritance pattern are not well-established based on the available information. The gene shows relatively low constraint to loss-of-function variants, suggesting some tolerance to protein disruption.

ResearchSummary from RefSeq
MultiplemechanismLOEUF 1.41
Clinical Summary— SERTM1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.00) despite low pLI — interpret in context.
📋
ClinVar Variants
48 unique Pathogenic / Likely Pathogenic· 14 VUS of 64 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.41LOEUF
pLI 0.492
Z-score 1.26
OE 0.00 (0.00–1.41)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
1.03Z-score
OE missense 0.61 (0.46–0.81)
34 obs / 55.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.00–1.41)
0≤0.351.4
Missense OE0.61 (0.46–0.81)
0≤0.61.4
Synonymous OE1.01
0≤1.21.6
LoF obs/exp: 0 / 1.9Missense obs/exp: 34 / 55.6Syn Z: -0.05
DN
0.6743th %ile
GOF
0.73top 25%
LOF
0.3357th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

64 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic48
VUS14
48
Pathogenic
14
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
48
0
48
Likely Pathogenic
0
0
0
0
0
VUS
0
10
4
0
14
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total01052062

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SERTM1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients